Source code for utils.extract_atoms

#!/usr/bin/env python3

"""Module containing the ExtractAtoms class and the command line interface."""
import argparse
import re
from pathlib import Path
from biobb_common.configuration import settings
from biobb_common.generic.biobb_object import BiobbObject
from import file_utils as fu
from import launchlogger
from biobb_structure_utils.gro_lib.gro import Gro
from biobb_structure_utils.utils.common import PDB_SERIAL_RECORDS

[docs]class ExtractAtoms(BiobbObject): """ | biobb_structure_utils ExtractAtoms | Class to extract atoms from a 3D structure. Args: input_structure_path (str): Input structure file path. File type: input. `Sample file <>`_. Accepted formats: pdb (edam:format_1476), gro (edam:format_2033). output_structure_path (str): Output structure file path. File type: output. `Sample file <>`_. Accepted formats: pdb (edam:format_1476), gro (edam:format_2033). properties (dic - Python dictionary object containing the tool parameters, not input/output files): * **regular_expression_pattern** (*str*) - ("^D") Python style regular expression matching the selected atom names. * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files. * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist. Examples: This is a use example of how to use the building block from Python:: from biobb_structure_utils.utils.extract_atoms import extract_atoms prop = { 'regular_expression_pattern': '^D' } extract_atoms(input_structure_path='/path/to/myStructure.pdb', output_structure_path='/path/to/newStructure.pdb', properties=prop) Info: * wrapped_software: * name: In house * license: Apache-2.0 * ontology: * name: EDAM * schema: """ def __init__(self, input_structure_path, output_structure_path, properties=None, **kwargs) -> None: properties = properties or {} # Call parent class constructor super().__init__(properties) self.locals_var_dict = locals().copy() # Input/Output files self.io_dict = { "in": {"input_structure_path": input_structure_path}, "out": {"output_structure_path": output_structure_path} } # Properties specific for BB self.regular_expression_pattern = properties.get('regular_expression_pattern', '^D') # Check the properties self.check_properties(properties) self.check_arguments()
[docs] @launchlogger def launch(self) -> int: """Execute the :class:`ExtractAtoms <utils.extract_atoms.ExtractAtoms>` utils.extract_atoms.ExtractAtoms object.""" # Setup Biobb if self.check_restart(): return 0 self.stage_files() # Business code extension = Path(self.io_dict['in']['input_structure_path']).suffix.lower() if extension.lower() == '.gro': fu.log('GRO format detected, extracting all atoms matching %s' % self.regular_expression_pattern, self.out_log) gro_st = Gro() gro_st.read_gro_file(self.io_dict['in']['input_structure_path']) gro_st.select_atoms(self.regular_expression_pattern) if gro_st.num_of_atoms: fu.log('%d atoms found writting GRO file' % gro_st.num_of_atoms, self.out_log, self.global_log) gro_st.write_gro_file(self.io_dict['out']['output_structure_path']) else: fu.log('No matching atoms found writting empty GRO file', self.out_log, self.global_log) open(self.io_dict['out']['output_structure_path'], 'w').close() else: fu.log('PDB format detected, extracting all atoms matching %s' % self.regular_expression_pattern, self.out_log) # Direct aproach solution implemented to avoid the # issues presented in commit message (c92aab9604a6a31d13f4170ff47b231df0a588ef) # with the Biopython library atoms_match_cont = 0 with open(self.io_dict['in']['input_structure_path'], "r") as input_pdb, open(self.io_dict['out']['output_structure_path'], "w") as output_pdb: for line in input_pdb: record = line[:6].upper().strip() if len(line) > 10 and record in PDB_SERIAL_RECORDS: # Avoid MODEL, ENDMDL records and empty lines pdb_atom_name = line[12:16].strip() if, pdb_atom_name): atoms_match_cont += 1 output_pdb.write(line) if atoms_match_cont: fu.log('%d atoms found writting PDB file' % atoms_match_cont, self.out_log, self.global_log) else: fu.log('No matching atoms found writting empty PDB file', self.out_log, self.global_log) self.return_code = 0 ########## # Copy files to host self.copy_to_host() # Remove temporal files self.tmp_files.append(self.stage_io_dict.get("unique_dir")) self.remove_tmp_files() self.check_arguments(output_files_created=True, raise_exception=False) return self.return_code
[docs]def extract_atoms(input_structure_path: str, output_structure_path: str, properties: dict = None, **kwargs) -> int: """Execute the :class:`ExtractAtoms <utils.extract_atoms.ExtractAtoms>` class and execute the :meth:`launch() <utils.extract_atoms.ExtractAtoms.launch>` method.""" return ExtractAtoms(input_structure_path=input_structure_path, output_structure_path=output_structure_path, properties=properties, **kwargs).launch()
[docs]def main(): """Command line execution of this building block. Please check the command line documentation.""" parser = argparse.ArgumentParser(description="Remove the selected ligand atoms from a 3D structure.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999)) parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string") # Specific args of each building block required_args = parser.add_argument_group('required arguments') required_args.add_argument('-i', '--input_structure_path', required=True, help="Input structure file name") required_args.add_argument('-o', '--output_structure_path', required=True, help="Output structure file name") args = parser.parse_args() config = args.config if args.config else None properties = settings.ConfReader(config=config).get_prop_dic() # Specific call of each building block extract_atoms(input_structure_path=args.input_structure_path, output_structure_path=args.output_structure_path, properties=properties)
if __name__ == '__main__': main()